Relationship of Microbial Activity with Soil Properties in Banana Plantations in Venezuela

Round 1

Reviewer 1 Report

I have reviewed the manuscript entitled " Relationship of microbial activity with soil properties in banana plantations in Venezuela". The authors study relationship between microbial communities, soil physicochemical properties in different cropland area. The manuscript is generally well written. However, the some statistical analysis is problematic and the lack of details in the results section.

L70: should clarify which kind of microbial activity is discussed in the manuscript.

Fig 1b: raw data points and stdev is missing

L195-197: the authors should do ANOVA or similar analysis to compare the nematode variables

Fig 2: The logarithmic looks good but the author needs to show the stdev and number of replicates

L275: why the loading values have to be higher than 0.2, the author should explain the selection criteria of the variables

Fig3a: I don’t think the PCA has explained the variations between different soil sites very well, most of the data points were in the similar ellipse region

 

Author Response

Reviewer 1 comments

I have reviewed the manuscript entitled " Relationship of microbial activity with soil properties in banana plantations in Venezuela". The authors study relationship between microbial communities, soil physicochemical properties in different cropland area. The manuscript is generally well written. However, the some statistical analysis is problematic and the lack of details in the results section.

 

L70: should clarify which kind of microbial activity is discussed in the manuscript.

Authors: L70: Corrected. The following sentence was added: estimated indirectly by determining the basal respiration (O₂ consumption in the medium or the concentration of CO₂ released).

Fig 1b: raw data points and stdev is missing

Authors: Corrected. an appendix (Table A2) with the information of n, mean and stdev was added.

L195-197: the authors should do ANOVA or similar analysis to compare the nematode variables

Authors: Line 240. Corrected. The following sentence was added: …that no significant differences were found for both nematode variables (data not shown).

Authors: The Post Hoc Tests (Homogeneous Subsets were performed), whose results were not significant for the nematode variables for all the sites evaluated. An example of a sampling site (PL) is shown below:

PN
Duncan
	N	Subset for alpha = .05
NP		1
L	4	73,7
H	4	92,95
Sig.		0,164
Means for groups in homogeneous subsets are displayed.
a Uses Harmonic Mean Sample Size = 4.000.
FLN
Duncan
	N	Subset for alpha = .05
NP		1
H	4	7,125
L	4	26,325
Sig.		0,165
Means for groups in homogeneous subsets are displayed.
a Uses Harmonic Mean Sample Size = 4.000.

 

Fig 2: The logarithmic looks good but the author needs to show the stdev and number of replicates

Authors: Line 601. an appendix (Table A1) with the information of n, mean and stdev was added

L275: why the loading values have to be higher than 0.2, the author should explain the selection criteria of the variables

Authors: L289: Corrected. The following sentence was added: Only corresponding loadings greater than the absolute value of 0.2 are the best option for model interpretation and revealing the most important variables regarding the explanation of the response [41].

Citation: Yang, B.; Zhang, C.; Cheng, S.; Li, G.; Griebel, J.; Neuhaus, J. Novel Metabolic Signatures of Prostate Cancer Revealed by 1H-NMR Metabolomics of Urine. Diagnostics 2021, 11, 149. https://doi.org/10.3390/diagnostics1102014

Fig3a: I don’t think the PCA has explained the variations between different soil sites very well, most of the data points were in the similar ellipse region

Authors: We are agreed.  L280: Corrected. The following sentence was added: PLS-DA could not distinguish high and low productivity levels of banana (Figure 3a). The first two main components (PC) explained 49.9% of the variables; however, no trends were detected in banana productivity differences

Author Response File: Author Response.pdf

Reviewer 2 Report

 

The manuscript entitled “Relationship of microbial activity with soil properties in banana plantations in Venezuela” authored by Olivares et al., is a microbial diversity study in the banana fields. The reviewer gone through the manuscript and found that the manuscript is presented as per journal guidelines, the contents of the manuscript is in a defined format, and the table and figures are presented appropriately. The followings are the query and suggestions for improving the quality of the manuscript-

1.      Please follow the same naming style for all authors

2.      Delete the keywords “Free-living nematodes and soil” author should add “soil microbes” in the keywords

3.      Briefly add the nutritional and economic value of the banana with a suitable citation

4.      Rewrite “The most recent works related to the quality of …González-García et al. [12, 42 13].” For better clarity line no. 40-43

5.      Delete “microbes” in line no. 46

6.      Rewrite the sentence “Precisely these organisms constitute … soil aggregates stable [14,15]” line no. 47-53 for better clarity, it is better to write in small sentences

7.      Table .1 is ok,  it will be better to add the average yield in different farms

8.      Method and material are described nicely

9.      Figure 1 is ok

10.  Check for “Figure 2a” it should be “Figure 2A” same with figure 2b and 3 also made correction

11.  Figure 2 and 3 are ok

12.  Table 2 and 3 are ok

13.  Figure 4 and 5 are ok

14.  The results and discussion section is written nicely and the interpretation of results in the discussion is ok.

15.  The conclusion section should be modified for soundness

Overall, the manuscript is presented in a nice but there are many minor grammatical mistakes and the use of unscientific words which can be improved. The present study will help in the identification of beneficial soil microbial groups for banana yield improvement. 

Author Response

The manuscript entitled “Relationship of microbial activity with soil properties in banana plantations in Venezuela” authored by Olivares et al., is a microbial diversity study in the banana fields. The reviewer gone through the manuscript and found that the manuscript is presented as per journal guidelines, the contents of the manuscript is in a defined format, and the table and figures are presented appropriately. The followings are the query and suggestions for improving the quality of the manuscript-

 

1. Please follow the same naming style for all authors

Authors: Corrected.

2. Delete the keywords “Free-living nematodes and soil” author should add “soil microbes” in the keywords

Authors: Corrected.

3. Briefly add the nutritional and economic value of the banana with a suitable citation

Authors: L35. Corrected. The following sentence was added: Its composition highlights its richness in carbohydrates (20%), and an important source of Potassium, Vitamin C, and Iron.

4. Rewrite “The most recent works related to the quality of …González-García et al. [12, 42 13].” For better clarity line no. 40-43

Authors: L35. Corrected. The following sentence was added: The most recent studies in Venezuela are those of

5. Delete “microbes” in line no. 46

Authors: L46. Corrected.

6. Rewrite the sentence “Precisely these organisms constitute … soil aggregates stable [14,15]” line no. 47-53 for better clarity, it is better to write in small sentences

Line 54: Corrected. The following sentence was added: These organisms are represented by unicellular and microscopic forms, nematodes, insect larvae, earthworms and arthropods, whose function is to transform all organic and inorganic compounds in the soil with direct or indirect influence on properties such as soil porosity, water transport and the union of particles for the formation of stable soil aggregates [14,15].

7. Table .1 is ok, it will be better to add the average yield in different farms

Authors: Corrected.

8. Method and material are described nicely

Authors: Thanks

9. Figure 1 is ok

Authors: Thanks

10. Check for “Figure 2a” it should be “Figure 2A” same with figure 2b and 3 also made correction

Authors: Corrected.

11. Figure 2 and 3 are ok

Authors: Thanks

12. Table 2 and 3 are ok

Authors: Thanks

13. Figure 4 and 5 are ok

Authors: Thanks

14. The results and discussion section is written nicely and the interpretation of results in the discussion is ok.

Authors: Thanks

15. The conclusion section should be modified for soundness

Authors: Corrected.

Overall, the manuscript is presented in a nice but there are many minor grammatical mistakes and the use of unscientific words which can be improved. The present study will help in the identification of beneficial soil microbial groups for banana yield improvement.

Authors: Thanks

Reviewer 3 Report

 

This manuscript submitted to ‘Sustainability’ deals with relationship of microbial activity with soil properties in banana plantations in Venezuela. The authors succeeded in demonstrating how soil properties influence the production of a complex and variable system there. It harnessed machine learning algorithms as Debiased Sparse Partial Correlation (DSPC), Partial Least Squares - Discriminant Analysis (PLS-DA) and Random Forest to explore a variety of variables in 6 agricultural fields located in two of the main banana production areas of Venezuela. The research article is full of many relevant references and statistical analyzes that are supportive and useful in analyzing the results. Yet, I do NOT understand why they did not standardize their sampling procedures (e.g., number of samples) across the surveyed fields, although the study considered the same number of undisturbed samples (36) obtained with an Uhland type sampler (mean depth 29.6 ± 17.6 cm) to obtain the saturated hydraulic conductivity (Ks, cm.h^-1). The presented figures are generally OK but some needs to have more explanation especially for abbreviation, e.g. Figure 3. needs more clarification for the rest of symbols there. Moreover, the writing style is somewhat awkward with some misprints, grammar faults, and construction of some sentences in this manuscript, to name but few:

1)    “For determining the relative importance of different order and genre nematodes” Should be ““For determining the relative importance of different nematode orders and genera”.

2)    “with 4 four replicated” 4 is repeated.

3)    “In studies recent, no significant…”  Should be “In recent studies, no significant…” 

4)    respiration (r=1.00; p= 0.014), and NO3 (r= 1.00; p= 0.032). I wonder how the correlation coefficient reached its maximum point with such relatively modest statistical probability level.

5)    “but in soil science as well. general.” The word “general” is alone !!

6)     “and employment to populations rural order/genre in banana” misprints and grammar faults.

7)    According to results, phytonematodes predominate in the banana system evaluated with ? (were) eleven important genera (Figure 1a), with Rotylenchulus

Therefore, I would suggest rewriting the manuscript and resubmitting it again.

 

 

Author Response

This manuscript submitted to ‘Sustainability’ deals with relationship of microbial activity with soil properties in banana plantations in Venezuela. The authors succeeded in demonstrating how soil properties influence the production of a complex and variable system there. It harnessed machine learning algorithms as Debiased Sparse Partial Correlation (DSPC), Partial Least Squares - Discriminant Analysis (PLS-DA) and Random Forest to explore a variety of variables in 6 agricultural fields located in two of the main banana production areas of Venezuela. The research article is full of many relevant references and statistical analyzes that are supportive and useful in analyzing the results. 

 

Yet, I do NOT understand why they did not standardize their sampling procedures (e.g., number of samples) across the surveyed fields, although the study considered the same number of undisturbed samples (36) obtained with an Uhland type sampler (mean depth 29.6 ± 17.6 cm) to obtain the saturated hydraulic conductivity (Ks, cm.h^-1).

 

Authors: Soil and banana productivity samplings were carried out according to the guidelines of Rosales et al. 2008. In that document, a group of international banana experts established the following:

 

Each site (high and low productivity) will be divided into sampling areas of approximately 1 hectare; the number will depend on the size of the farm. If the farms to be studied are smaller than 10 hectares, it is recommended to only take a sampling area in the "high" site and one in the "low productivity" site. On farms of 10 to 25 hectares, two sampling areas per site are recommended. If the farm has between 26 and 50 hectares, 3 areas per "high" site and 3 per "low productivity" site would be made. Farms with more than 50 hectares would be diagnosed with 4 sampling points in high production sites and 4 in low production or vigor sites.

 

23. Rosales, F.E.; Pocasangre, L.E.; Trejos, J.; Serrano, E.; Peña, W. Guía de diagnóstico de la calidad y salud de suelos bananeros. Bioversity International: Roma. Italy. 2008; pp. 48-80. https://www.bioversityinternational.org/fileadmin/user_upload/online_library/publications/pdfs/1375.pdf

The presented figures are generally OK but some needs to have more explanation especially for abbreviation, e.g. Figure 3. needs more clarification for the rest of symbols there.

Authors: Line 427. The following sentence was added: Figure 3. A) Scores plot between the Component 1 and Component 2 of the PLS-DA. Note: Data code composed of three digits, the first digit is the site (PL, KA, BA, SM, PA, and CH), followed by the level of productivity: (H) High and (L) low, and finally the repetition number (1-4).

 Moreover, the writing style is somewhat awkward with some misprints, grammar faults, and construction of some sentences in this manuscript, to name but few:

1)    “For determining the relative importance of different order and genre nematodes” Should be ““For determining the relative importance of different nematode orders and genera”.

 

Authors: Line 199: corrected.

 

2)    “with 4 four replicated” 4 is repeated.

Authors: Line 149. corrected.

3)    “In studies recent, no significant…”  Should be “In recent studies, no significant…” 

Authors: Line 525: corrected.

4)    respiration (r=1.00; p= 0.014), and NO3 (r= 1.00; p= 0.032). I wonder how the correlation coefficient reached its maximum point with such relatively modest statistical probability level.

 

Authors: Line 532: Here we present the results of the deviant sparse partial correlation (DSPC) algorithm that is based on the recently proposed deparsified graph lasso modeling procedure (Jankova, 2015). A key assumption underlying our modeling strategy is that the number of true connections between variables is much smaller than the available sample size, that is, the true network of partial correlations between variables is sparse.

 This assumption is strongly supported by both empirical evidence and theoretical calculations (Gardner et al., 2003; Jeong et al., 2001; Leclerc, 2008). Under this assumption, DSPC reconstructs a graphical model and provides partial correlation coefficients and P-values ​​for each pair of variables in the data set. Therefore, DSPC allows to discover the connectivity between many variables using fewer samples. The results can be visualized as weighted networks where the nodes represent the variables, and the edges represent partial correlation coefficients or the associated P-values.

5)    “but in soil science as well. general.” The word “general” is alone !!

 

Authors: Line 90: corrected.

6)     “and employment to populations rural order/genre in banana” misprints and grammar faults.

Authors: Line 37: corrected. the phrase was deleted

Line 233: order/genre was deleted

7)    According to results, phytonematodes predominate in the banana system evaluated with ? (were) eleven important genera (Figure 1a), with Rotylenchulus

Therefore, I would suggest rewriting the manuscript and resubmitting it again.

Authors: Line 280. corrected. According to results, Phytonematodes predominate in the banana system being eleven important genera (Figure 1A), like Rotylenchulus

Authors: Corrections to grammatical errors in the manuscript were made

 

Reviewer 4 Report

Only some comments are included in the ms. 

In general, the ms is valuable. 

Comments for author File: Comments.pdf

Author Response

In general, the ms is valuable. 

Authors: Thanks

Line 18: delete and

Authors: Corrected.

Citation (1) I am not sure if this ms is the most appropriate to take the general overview of the banana plantation in the world.  The article is related with banana grow in Venezuela.

Authors: Corrected. added this new reference:

Martínez-Solórzano, G.E.; Rey-Brina, J.C. Bananos (Musa AAA): Importance, production, and trade in Covid-19 ti-mes. Agronomía Mesoamericana 2021, 32(3), 1034-1046. http://dx.doi.org/10.15517/am.v32i3.43610

Round 2

Reviewer 1 Report

the revised version looks good